Deus ex Machina
by A Modern Sophocles
Summary: Naruto is almost killed by the villagers, but is saved by Jiraiya. He then trains him all around the elemental nations, until Naruto is as powerful or more than Jiraiya. He then becomes a shadow named "Deus ex Machina" and helps people in need. What will happen when he returns to Konoha. Eventual godlike Naruto. Naruto X Harem. Maybe some lemons later.


**Disclaimer: I do not own Naruto or any elements of that story, but I do own the rights to any original characters or original techniques that may be displayed in this story.**

Chapter 1: The Seal Master and the Apprentice

Naruto's Age: Five Years Old

A figure could be seen streaking across the village, running with all of his might. At first glance, one might think that he was simply a kid playing a game of tag, or some other childish game. But this particular child had never had the opportunity to play a game of tag; he was never allowed to play a game, and he had never had a friend.

Behind him, there was a large group of villagers chasing him with anything and everything that they could find. They were armed with kitchen knives and pitchforks and curtain rods and everything else they could find around their houses. There were even a few low-level shinobi who were more heavily armed.

In his frenzy to escape from the mob, he made a wrong turn and ended up in an alley that ended at a building. The only way out was back the way he came in, but by the time he turned to get out, the hostile group of villagers had blocked his exit. He quickly looked around to see if there was any way he could climb out of the alley.

He spied a ledge about eight feet up. He jumped with all his might and grabbed the ledge with one arm. He thought that he might just escape until his ankle was grabbed from below and pulled him down, back into the alley. He was then repeatedly stabbed and gashed with knives and other pointed object. He just curled up into a ball, and waited for it to end. At this point he didn't care which way it ended, either with him waking up in the hospital or not waking up at all, he just wanted it to stop.

After almost half an hour of being beaten and stabbed, they left him in a pool of blood that extended from the back of the alley all the way into the main street, twenty feet away. Eventually, an ANBU with a dog mask was passing by in the street and saw the pool of blood coming from the alley. He found a child lying in a pool of blood in the back corner of the alley, hidden in the shadows.

He knew that he could not take him to the hospital. He was near death and fading fast, but the hospital was the worst place that he could take him. Over the years, the hospital staff has inconspicuously demonstrated their animosity toward him by mistreating all his injuries. If it were not for his incredible healing ability, he would be permanently disfigured by bones set incorrectly and other cases of malpractice.

Instead, the dog-masked ANBU took him to the Hokage's office. He hoped that this would convince the Hokage to do something about him. It was obvious that his current policy regarding Naruto wasn't working.

When he arrived at the Hokage's office, he realized that he was currently returning from a diplomatic meeting with Kirigakure. He was scheduled to be back later that day, however, his secretary was there.

"When the Hokage returns, please make sure this boy is placed in his care. If you don't do this, I'm certain he will fire you faster than you can say 'Wrongful Termination.'" The dog-masked ANBU said to the secretary. "I have an important ANBU meeting to be at and I'm already three hours late."

The secretary sweatdropped at his Chronic tardiness. "Will do," replied the secretary. However, little did anyone know that she was a member of the majority of the village that hated Naruto for the circumstances of his birth. Also, she advocated a more violent solution than most when it came to dealing with him.

As soon as the ANBU left, the secretary stormed out of the office, with Naruto still in her hands. She was agitated that he had survived what she had thought would be a fatal attack on him. She hurried around the village, raisin another mob to make sure that he would not longer be counted in the world of the living.

The mob followed her around Konoha and eventually they started to climb the Hokage monument. She planned to kill Naruto in a way that would be be very fitting of the crimes he had done against them, killing their friends, family, and especially the Yondaime Hokage. She planned to throw him off the top of the Hokage monument, from the top of the fourth Hokage's head. There was no way even a demon-child could survive a fall from that height.

O-O-O-O-O

Jiraiya was back in Konoha for the first time in five years. Currently he has doing his "research" outside a hot spring near the Hokage monument. Jiraiya was widely known as a super-pervert, but right now he was not just leering at the naked ladies in the hot springs for himself, he was rapidly scribbling notes to write his newest Icha Icha book that satisfied closet perverts everywhere.

As he was watching with a giant grin on his face, he saw an orange streak headed toward the ground closer to the Hokage monument. He sprinted over to where it was about to hit the ground and he saw that it was a small boy. He jumped up into the air, caught him, and slid down a tree to slow him down.

As he look more closely at him, he saw that he was covered in bruises and cuts and his clothing was hanging in tatters. Then he noticed the bright, spiky, yellow hair and whisker marks on his cheeks and he realized that he was Naruto Uzumaki-Namikaze, the son of his favorite student and his godson.

Furious, he realized that he needed to have a talk with is his former teacher about how the village was treating Naruto. Sarutobi had said that he would look out for Naruto, and that Jiraiya needed to maintain his spy network. Now he was determined to do something for his grandson other than leave him in the village where he would sooner rather than later be killed in retribution for the Kyuubi attack.

Jiraiya left Naruto in his apartment that he stayed in when returned to Konoha and went to formulate a plan to get Naruto out of the village.

O-O-O-O-O

When Naruto woke up he did not see the familiar sight of the hospital ceiling. 'I guess I didn't survive that beating. Oh well, there was nothing for me to live for anymore anyways.' He thought. 'But why does the afterlife look like a crummy old apartment.

While he was thinking this, and old man with long, spiky white hair, wearing green pants, a green shirt, and a red vest, and a Konoha forehead protector entered. "Hello, Naruto. My name is Jiraiya, and I am here to help you. I understand all the pain you've been through in you short life and I want to help you."

"Why do you want to help me. No one except the old man and Teuchi and Ayame even acknowledge that I exist."

"First, I knew your father. And yes," Jiraiya said as Naruto started to ask him the question that he knew was coming, "I will tell you who he was. I will also tell you the identity of your mother. But first, I going to tell you why the villagers hate you so much. But first, know that I do not that you for this. Do you know the history of the Kyuubi attack?"

"Yes, the Kyuubi came to destroy Konoha and it killed a lot of people. Bu then the Yondaime Hokage, the greatest shinobi ever, sacrificed himself to kill the Kyuubi and save everyone in the village. My goal is to be the Hokage and to be as cool as the fourth Hokage!" Naruto said this with increasing intensity and by the end, he was shouting.

"Quiet down kid. I won't tell you anything if you keep shouting like this." Naruto quieted down immediately at this ultimatum. "The Kyuubi, and all the bijuu, cannot be killed, so the Yondaime had to seal it in someone. A person with a bijuu sealed in them is called a jinchuuriki. For a seal to contain the Kyuubi, it must be performed on an infant."

"Before you ask, yes, you were that infant. But more importantly, the Yondaime performed that sealing technique on HIS SON. Naruto, you are the son of the fourth Hokage."

Naruto did not know whether to be overjoyed or severely depressed. "So this means that the villagers were right when they called me a demon. I guess I deserve all the punishments that I get. I killed so many people's friends and family-"

Jiraiya interrupted him, "No, the Kyuubi is sealed inside of you. It was your father's dream that you be revered as a hero for keeper the Kyuubi at bay. You are the jailor.

Anyways, continuing where we left off, your mother was Kushina Uzumaki, but she was never officially announced as the Hokage's wife. AS you know, your father had many enemies, and he didn't want them to be targeting your mother while she was pregnant. But a very, very well kept secret is that your mother was the previous host of the Kyuubi."

"Do you mean that she was persecuted like me?"

"No, nobody knew that she was jinchuuriki, so her life was a lot better.

Well that's enough of the past; I'm going to make sure that your life will become a lot better. First, we are going to leave Konoha. Once we are significantly far away, I will tell you the rest of my plan. I'm going to put you and me under a henge so no one notices us leaving."

The two then transformed into two nondescript civilians and started for the gate of the village. Immediately after they left the gate, the ANBU with the dog mask, the one who saved Naruto earlier confronted them.

"Who are you and what are you doing with Naruto?"

"Who wants to know?"

"I try to look out for Naruto. I tracked him to your apartment, and then I saw you leaving and assumed you must be under a henge."

"I'll answer both questions, if you do me one small favor."

"Done." Replied the ANBU

"Naruto is not safe here. I'm going to keep him safe and train him to be a greater shinobi than either of his parents."

The dog ANBU, knowing who Naruto's parents were was slightly shocked. "Who could possibly train him to be better than the Yondaime?"

Jiraiya then undid the henge on himself. "Why only the Yondaime's teacher." The dog ANBU just stood there in shock at seeing the legendary Toad Sage. "And plus, you wouldn't want me to stop writing those orange novels you love so much." The dog ANBU just sweatdropped at that. "You are allowed to tell the Hokage, but tell him he won't know where Naruto is going, and if he makes in public knowledge that he is with me, I'll make sure he never returns to Konoha."

The ANBU was more than slightly shocked at his staunch defense of Naruto. "Why are you doing so much for him."

"He is my godson, and I have failed in my duties up to this point." Jiraiya said looking somewhat ahamed. Now go."

O-O-O-O-O

"So Jiraiya took Naruto to train him and keep him safe. This is probably for the best. I WILL oblige his wish for this to be kept secret. I just hope that he will come back to Konoha, and that we can publicly acknowledge his genealogy. You can go now dog." The Hokage dismissed the dog ANBU to go back to his duties.

O-O-O-O-O

The next day

"Naruto, the first technique I want to show you is going to very useful to you. It will help you progress many times faster than a usual person could. It is called the shadow clone jutsu. This allows you to create multiple solid copies of yourself. The most useful part is that you retain any knowledge of what they do, so they are amazing for training."

"Jiraiya-sensei, if this technique is so useful, why doesn't most people use it?"

"Ah, that brings me to it's one downside. It uses a lot of chakra, but because of your Uzumaki heritage and the Kyuubi, you have very large chakra reserves."

Jiraiya the proceeded to show him the unique hand sign of two fingers on each hand making a right angle. "Make as many shadow clones as you can."

Jiraiya regretted that statement as soon as he saw how many shadow clones he created. There were, in that small clearing, six hundred short five year old ninjas with bright yellow hair.

"Okay, I did not expect that many, but it would be a shame to have the go to waste." Then addressing the mass of clones, he said, "Divide yourselves into six groups of one hundred, and in each group five groups of twenty."

Then, making five clones of himself, Jiraiya and his clones each took a group aside and began to work on one technique with each group. The origina went with one group of clones. "Jiraiya-sensei, why will you not be teaching me directly?"

"I have a highly advanced technique that is very dangerous that I want to show you; it is so dangerous that I only want clones to use it until you've mastered it."

O-O-O-O-O

With Group One

"Okay clones, your mission is chakra control. This will help you to be able to use more advanced techniques and to use less chakra when you do so. The first exercise is tree climbing. You must apply a constant stream of chakra to your feet to stick to the tree. Too much and you will fly off: too little and you won't stick. Get the idea?"

"Yes sensei," the clones chanted together.

"One more twist to make this interesting. We will have a tournament. The first twenty to make it up to the top of the tree will get to move on the the more advanced exercise. The rest of you will be dispelled by me, adding not only to Naruto's chakra control, but also to the lucky twenty clones to help them with the advanced exercise. The first four to complete the advanced exercise will get to have a taijutsu spar for fun.

O-O-O-O-O

With Groups Two and Three

"Okay group two, you plus four lucky clones from group three are going to practice the basics katas of two different styles. The first one is the deflecting fist, a taijutsu style that I think will be perfect for you. The general concept is to mostly defend and block the enemies attacks. However, you will block them in a way that will throw them off balance, leaving them open for a counter-attack. This style will be great for you because you can outlast your opponents with your impressive stamina.

The second style that you will be learning is the fox style. It uses many feints to keep your opponent constantly off-balance.

Group three, watch and when they are done, they will dispel, and grant you their knowledge of these two styles. With the 96 of you that remain we will have a tournament using only taijutsu. There will be two brackets, one of 64, and another of 32, and the winners will face off."

O-O-O-O-O

With Group Four

"You clones are the lucky ones; you get to do the exciting stuff, ninjutsu and fuuinjutsu. I will show you some basic elemental have to learn the basic jutsu first before you can do the awesome ones." **(A/N: It would help if you guys could leave cool jutsu and seals that you want to have me use. I am very lazy and I'm sure you can do a better job than me.)**

O-O-O-O-O

With Group Five

"You hundred clones will be reading books on many techniques including jutsu theory, fuuinjutsu, and even some novels to enhance your social skills. This will help you a lot when you get older.

O-O-O-O-O

And so went Naruto's training for the next six months. He progressed by leaps and bounds in all areas. The area he improved most in was Fuuinjutsu. By now, he was approaching mastery of seals, almost on Jiraiya's level. Jiraiya suspected that his natural ability in seals was due to his Uzumaki heritage.

His taijutsu skills were high chunin, and his ninjutsu was low jonin. The cornerstone of his jutsu repertoire was his fathers unique jutsu, the rasengan. Everyday, the original Jiraiya would train Naruto's hundred clones. By this point he had mastered it up to how far his father had taken it. However, it was still unfinished as his father left it.

Unbeknownst to Jiraiya, or anyone else for that matter, one night, Naruto had created twenty clones to perform a top secret infiltration mission. The target: Konoha, more specifically, his father's estate. He gave them a sample of his blood to unlock any blood seals, which he expected there to be.

From this recon mission he obtained one scroll, but this one scroll was so great that it allowed a man to kill half if Iwa's forces in one night. He had been practicing the flying thunder god technique after training with Jiraiya everyday. However, he started to become bored.

"Jiraya-sensei, how long will we be doing the same thing; I'm getting bored."

"Listen while you're my apprentice, so you do what I say until I say you're done or you're the best ninja in the world."

"Come on pervy-sage, how will I know if I'm the the best ninja in the world."

Jiraiya paused for a second to think up some impossible task for him to accomplish. "You can leave my service when you can perform your father's signature jutsu better than he could: without seals where you teleport and without the yellow flash giving away your presence."

"All right, it may take me a while but you better believe that I can do it."

"Jiraiya sweatdropped at his antics. 'I didn't mean for him to take it seriously.' "Don't get a swelled hubris already. After only six months, you haven't improved THAT much just yet. But there will actually be a change in your training. We will search for an old friend of mine to teach you some things that I cannot.

And with that they set off to find Tsunade, the slug princess, the master medic of the Sennin.

**And that's a wrap. I have tried fanfiction a couple times before, but none were good enough to publish. Just to let you know, I have this planned out pretty far in advance, but if there are any little things you want me to make happen I can do it. For now, in the comments leave what summoning contract you want Naruto to have.**

**Until Next Time**

**-Eli**


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